[2023-06-27 02:56:44,104] [INFO] DFAST_QC pipeline started.
[2023-06-27 02:56:44,106] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 02:56:44,106] [INFO] DQC Reference Directory: /var/lib/cwl/stgbeba38d2-72ba-4d8d-bfad-0e655ca0d1c5/dqc_reference
[2023-06-27 02:56:45,313] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 02:56:45,314] [INFO] Task started: Prodigal
[2023-06-27 02:56:45,314] [INFO] Running command: gunzip -c /var/lib/cwl/stgf27934a8-423d-4e02-a610-90e834da65f5/GCA_026169035.1_ASM2616903v1_genomic.fna.gz | prodigal -d GCA_026169035.1_ASM2616903v1_genomic.fna/cds.fna -a GCA_026169035.1_ASM2616903v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 02:56:50,724] [INFO] Task succeeded: Prodigal
[2023-06-27 02:56:50,725] [INFO] Task started: HMMsearch
[2023-06-27 02:56:50,725] [INFO] Running command: hmmsearch --tblout GCA_026169035.1_ASM2616903v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbeba38d2-72ba-4d8d-bfad-0e655ca0d1c5/dqc_reference/reference_markers.hmm GCA_026169035.1_ASM2616903v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 02:56:51,006] [INFO] Task succeeded: HMMsearch
[2023-06-27 02:56:51,008] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf27934a8-423d-4e02-a610-90e834da65f5/GCA_026169035.1_ASM2616903v1_genomic.fna.gz]
[2023-06-27 02:56:51,039] [INFO] Query marker FASTA was written to GCA_026169035.1_ASM2616903v1_genomic.fna/markers.fasta
[2023-06-27 02:56:51,040] [INFO] Task started: Blastn
[2023-06-27 02:56:51,040] [INFO] Running command: blastn -query GCA_026169035.1_ASM2616903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeba38d2-72ba-4d8d-bfad-0e655ca0d1c5/dqc_reference/reference_markers.fasta -out GCA_026169035.1_ASM2616903v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:56:51,629] [INFO] Task succeeded: Blastn
[2023-06-27 02:56:51,634] [INFO] Selected 12 target genomes.
[2023-06-27 02:56:51,634] [INFO] Target genome list was writen to GCA_026169035.1_ASM2616903v1_genomic.fna/target_genomes.txt
[2023-06-27 02:56:51,636] [INFO] Task started: fastANI
[2023-06-27 02:56:51,636] [INFO] Running command: fastANI --query /var/lib/cwl/stgf27934a8-423d-4e02-a610-90e834da65f5/GCA_026169035.1_ASM2616903v1_genomic.fna.gz --refList GCA_026169035.1_ASM2616903v1_genomic.fna/target_genomes.txt --output GCA_026169035.1_ASM2616903v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 02:56:59,106] [INFO] Task succeeded: fastANI
[2023-06-27 02:56:59,107] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbeba38d2-72ba-4d8d-bfad-0e655ca0d1c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 02:56:59,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbeba38d2-72ba-4d8d-bfad-0e655ca0d1c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 02:56:59,122] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 02:56:59,122] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 02:56:59,123] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	94.4694	658	797	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	94.4692	657	797	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	94.4559	654	797	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	80.5157	355	797	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	79.0371	72	797	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.8147	52	797	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.669	66	797	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	77.6188	50	797	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	77.5427	129	797	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	77.3971	159	797	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.6984	51	797	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 02:56:59,124] [INFO] DFAST Taxonomy check result was written to GCA_026169035.1_ASM2616903v1_genomic.fna/tc_result.tsv
[2023-06-27 02:56:59,125] [INFO] ===== Taxonomy check completed =====
[2023-06-27 02:56:59,125] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 02:56:59,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbeba38d2-72ba-4d8d-bfad-0e655ca0d1c5/dqc_reference/checkm_data
[2023-06-27 02:56:59,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 02:56:59,156] [INFO] Task started: CheckM
[2023-06-27 02:56:59,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026169035.1_ASM2616903v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026169035.1_ASM2616903v1_genomic.fna/checkm_input GCA_026169035.1_ASM2616903v1_genomic.fna/checkm_result
[2023-06-27 02:57:22,774] [INFO] Task succeeded: CheckM
[2023-06-27 02:57:22,776] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 02:57:22,797] [INFO] ===== Completeness check finished =====
[2023-06-27 02:57:22,797] [INFO] ===== Start GTDB Search =====
[2023-06-27 02:57:22,798] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026169035.1_ASM2616903v1_genomic.fna/markers.fasta)
[2023-06-27 02:57:22,798] [INFO] Task started: Blastn
[2023-06-27 02:57:22,798] [INFO] Running command: blastn -query GCA_026169035.1_ASM2616903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeba38d2-72ba-4d8d-bfad-0e655ca0d1c5/dqc_reference/reference_markers_gtdb.fasta -out GCA_026169035.1_ASM2616903v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:57:23,641] [INFO] Task succeeded: Blastn
[2023-06-27 02:57:23,646] [INFO] Selected 6 target genomes.
[2023-06-27 02:57:23,646] [INFO] Target genome list was writen to GCA_026169035.1_ASM2616903v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 02:57:23,650] [INFO] Task started: fastANI
[2023-06-27 02:57:23,651] [INFO] Running command: fastANI --query /var/lib/cwl/stgf27934a8-423d-4e02-a610-90e834da65f5/GCA_026169035.1_ASM2616903v1_genomic.fna.gz --refList GCA_026169035.1_ASM2616903v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026169035.1_ASM2616903v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 02:57:27,430] [INFO] Task succeeded: fastANI
[2023-06-27 02:57:27,440] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 02:57:27,440] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_900539145.1	s__Blautia sp900539145	98.1301	650	797	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.09	98.22	0.85	0.80	3	conclusive
GCF_002222595.2	s__Blautia hansenii	94.4692	657	797	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.38	97.55	0.86	0.75	11	-
GCF_900120295.1	s__Blautia sp900120295	91.0522	656	797	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905201915.1	s__Blautia sp900555025	89.4713	555	797	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.26	99.26	0.76	0.76	2	-
GCA_900547685.1	s__Blautia sp900547685	88.0469	532	797	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013304445.1	s__Blautia sp900541955	79.4865	335	797	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.45	99.32	0.89	0.85	6	-
--------------------------------------------------------------------------------
[2023-06-27 02:57:27,442] [INFO] GTDB search result was written to GCA_026169035.1_ASM2616903v1_genomic.fna/result_gtdb.tsv
[2023-06-27 02:57:27,443] [INFO] ===== GTDB Search completed =====
[2023-06-27 02:57:27,485] [INFO] DFAST_QC result json was written to GCA_026169035.1_ASM2616903v1_genomic.fna/dqc_result.json
[2023-06-27 02:57:27,485] [INFO] DFAST_QC completed!
[2023-06-27 02:57:27,485] [INFO] Total running time: 0h0m43s